modules/vg_construct

Constructs a graph from a reference and variant calls or a multiple sequence alignment file

vggraphconstructfastavcfstructural variants

https://github.com/nf-core/modules/[...]/modules/nf-core/vg/construct

Description

Constructs a graph from a reference and variant calls or a multiple sequence alignment file

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`input`
`:list`

Either one or more VCF files containing different contigs or a multiple sequence alignment file

*.{vcf.gz,fa,fasta,fna,clustal}

`tbis`
`:list`

The index files for the VCF files

*.tbi

`insertions_fasta`
`:file`

A FASTA file containing insertion sequences (referred to in the VCF file(s))

*.{fa,fasta,fna}

`meta2`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta`
`:file`

The reference FASTA file (cannot be used in combination with msa, but is required when using vcfs)

*.{fa,fasta,fna}

`meta3`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`fasta_fai`
`:file`

The index of the reference FASTA file

*.fai

Output

name:type

description

pattern

`graph`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.vg`
`:file`

The constructed graph

*.vg

`versions_vg`

`${task.process}`
`:string`

The name of the process

`vg`
`:string`

The name of the tool

`vg 2>&1 | sed -n 's/.version v$[0-9.]$.*/\1/p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`vg`
`:string`

The name of the tool

`vg 2>&1 | sed -n 's/.version v$[0-9.]$.*/\1/p'`
`:eval`

The expression to obtain the version of the tool

Tools

vg
MIT

Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods.

github.com/vgteam/vg github.com/vgteam/vg/wiki

modules/vg_construct

Description

Input

`meta`
`:map`

`input`
`:list`

`tbis`
`:list`

`insertions_fasta`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fasta_fai`
`:file`

Output

`graph`

`meta`
`:map`

`*.vg`
`:file`

`versions_vg`

`${task.process}`
`:string`

`vg`
`:string`

`vg 2>&1 | sed -n 's/.version v\([0-9.]\).*/\1/p'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`vg`
`:string`

`vg 2>&1 | sed -n 's/.version v\([0-9.]\).*/\1/p'`
`:eval`

Tools

vg
MIT

maintainer

get in touch

modules/vg_construct

Description

Input

meta :map

input :list

tbis :list

insertions_fasta :file

meta2 :map

fasta :file

meta3 :map

fasta_fai :file

Output

graph

meta :map

*.vg :file

versions_vg

${task.process} :string

vg :string

vg 2>&1 | sed -n 's/.*version v\([0-9.]*\).*/\1/p' :eval

Topics

versions

${task.process} :string

vg :string

vg 2>&1 | sed -n 's/.*version v\([0-9.]*\).*/\1/p' :eval

Tools

vgMIT

maintainer

get in touch

`meta`
`:map`

`input`
`:list`

`tbis`
`:list`

`insertions_fasta`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fasta_fai`
`:file`

`graph`

`meta`
`:map`

`*.vg`
`:file`

`versions_vg`

`${task.process}`
`:string`

`vg`
`:string`

`vg 2>&1 | sed -n 's/.version v\([0-9.]\).*/\1/p'`
`:eval`

`versions`

`${task.process}`
`:string`

`vg`
`:string`

`vg 2>&1 | sed -n 's/.version v\([0-9.]\).*/\1/p'`
`:eval`

vg
MIT